20-4238611-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000678.4(ADRA1D):​c.1111+9236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,166 control chromosomes in the GnomAD database, including 2,568 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2568 hom., cov: 31)

Consequence

ADRA1D
NM_000678.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.866
Variant links:
Genes affected
ADRA1D (HGNC:280): (adrenoceptor alpha 1D) Alpha-1-adrenergic receptors (alpha-1-ARs) are members of the G protein-coupled receptor superfamily. They activate mitogenic responses and regulate growth and proliferation of many cells. There are 3 alpha-1-AR subtypes: alpha-1A, -1B and -1D, all of which signal through the Gq/11 family of G-proteins and different subtypes show different patterns of activation. This gene encodes alpha-1D-adrenergic receptor. Similar to alpha-1B-adrenergic receptor gene, this gene comprises 2 exons and a single intron that interrupts the coding region. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADRA1DNM_000678.4 linkuse as main transcriptc.1111+9236G>A intron_variant ENST00000379453.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADRA1DENST00000379453.6 linkuse as main transcriptc.1111+9236G>A intron_variant 1 NM_000678.4 P1

Frequencies

GnomAD3 genomes
AF:
0.180
AC:
27368
AN:
152048
Hom.:
2564
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.131
Gnomad AMI
AF:
0.170
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.306
Gnomad EAS
AF:
0.0394
Gnomad SAS
AF:
0.196
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.282
Gnomad NFE
AF:
0.216
Gnomad OTH
AF:
0.203
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.180
AC:
27402
AN:
152166
Hom.:
2568
Cov.:
31
AF XY:
0.176
AC XY:
13121
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.131
Gnomad4 AMR
AF:
0.172
Gnomad4 ASJ
AF:
0.306
Gnomad4 EAS
AF:
0.0395
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.171
Gnomad4 NFE
AF:
0.216
Gnomad4 OTH
AF:
0.201
Alfa
AF:
0.211
Hom.:
1931
Bravo
AF:
0.176
Asia WGS
AF:
0.113
AC:
395
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
7.0
DANN
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6076639; hg19: chr20-4219258; API